Multiple sequence alignment - TraesCS4A01G467600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G467600 chr4A 100.000 5790 0 0 1 5790 729682455 729688244 0.000000e+00 10693.0
1 TraesCS4A01G467600 chr4A 89.754 4314 334 46 457 4703 718929875 718925603 0.000000e+00 5419.0
2 TraesCS4A01G467600 chr4A 90.754 2585 175 33 2328 4880 729081004 729078452 0.000000e+00 3391.0
3 TraesCS4A01G467600 chr4A 86.675 2544 255 39 2753 5263 728429728 728427236 0.000000e+00 2743.0
4 TraesCS4A01G467600 chr4A 87.994 2124 216 22 2744 4845 729861798 729863904 0.000000e+00 2473.0
5 TraesCS4A01G467600 chr4A 86.941 2190 215 34 2728 4890 728831298 728833443 0.000000e+00 2394.0
6 TraesCS4A01G467600 chr4A 87.765 2027 192 22 476 2461 729859572 729861583 0.000000e+00 2318.0
7 TraesCS4A01G467600 chr4A 87.722 2028 192 23 476 2461 728431964 728429952 0.000000e+00 2313.0
8 TraesCS4A01G467600 chr4A 87.737 2006 197 25 456 2423 729532345 729530351 0.000000e+00 2296.0
9 TraesCS4A01G467600 chr4A 85.003 1907 244 32 2788 4674 729746080 729747964 0.000000e+00 1899.0
10 TraesCS4A01G467600 chr4A 92.832 1158 77 5 1170 2326 729084742 729083590 0.000000e+00 1674.0
11 TraesCS4A01G467600 chr4A 83.760 1601 218 28 3092 4674 729147705 729149281 0.000000e+00 1478.0
12 TraesCS4A01G467600 chr4A 87.268 1241 103 19 679 1892 729048580 729047368 0.000000e+00 1365.0
13 TraesCS4A01G467600 chr4A 86.285 1152 150 7 1170 2319 728829348 728830493 0.000000e+00 1245.0
14 TraesCS4A01G467600 chr4A 93.074 462 23 5 1 457 729532843 729532386 0.000000e+00 667.0
15 TraesCS4A01G467600 chr4A 86.607 448 48 6 18 457 729814993 729815436 8.720000e-133 484.0
16 TraesCS4A01G467600 chr4A 85.841 452 48 10 18 457 728432475 728432028 3.160000e-127 466.0
17 TraesCS4A01G467600 chr4A 85.778 450 48 10 20 457 729859063 729859508 4.090000e-126 462.0
18 TraesCS4A01G467600 chr4A 96.113 283 10 1 5342 5623 728426065 728425783 1.470000e-125 460.0
19 TraesCS4A01G467600 chr4A 82.857 455 67 9 6 457 729140205 729140651 1.170000e-106 398.0
20 TraesCS4A01G467600 chr4A 82.751 458 68 9 3 457 729743810 729744259 1.170000e-106 398.0
21 TraesCS4A01G467600 chr4A 91.756 279 18 1 457 730 729815477 729815755 3.270000e-102 383.0
22 TraesCS4A01G467600 chr4A 83.155 374 35 6 4912 5263 729863918 729864285 3.370000e-82 316.0
23 TraesCS4A01G467600 chr4A 94.845 194 9 1 456 648 729048776 729048583 9.430000e-78 302.0
24 TraesCS4A01G467600 chr4A 91.534 189 12 2 5331 5515 729864137 729864325 2.070000e-64 257.0
25 TraesCS4A01G467600 chr4A 93.289 149 10 0 5331 5479 728427384 728427236 2.720000e-53 220.0
26 TraesCS4A01G467600 chr4A 95.349 129 6 0 5211 5339 728427035 728426907 7.610000e-49 206.0
27 TraesCS4A01G467600 chr4A 79.514 288 26 15 4993 5263 730065840 730065569 2.140000e-39 174.0
28 TraesCS4A01G467600 chr4A 89.683 126 12 1 2338 2462 728830688 728830813 6.010000e-35 159.0
29 TraesCS4A01G467600 chr4A 82.386 176 21 6 5314 5479 729687542 729687717 1.680000e-30 145.0
30 TraesCS4A01G467600 chr4A 82.386 176 21 6 5088 5263 729687768 729687933 1.680000e-30 145.0
31 TraesCS4A01G467600 chr4A 85.496 131 13 6 5557 5681 729526005 729525875 1.310000e-26 132.0
32 TraesCS4A01G467600 chr4A 85.714 126 12 5 5557 5681 729077791 729077671 1.690000e-25 128.0
33 TraesCS4A01G467600 chr4A 81.560 141 20 3 5124 5263 728426062 728425927 1.710000e-20 111.0
34 TraesCS4A01G467600 chr4A 78.363 171 22 9 5350 5515 730065690 730065530 4.780000e-16 97.1
35 TraesCS4A01G467600 chr7A 91.532 3519 178 54 458 3916 9330484 9333942 0.000000e+00 4737.0
36 TraesCS4A01G467600 chr7A 82.727 1181 160 23 3902 5066 9334611 9335763 0.000000e+00 1011.0
37 TraesCS4A01G467600 chr7A 87.082 449 45 9 18 456 9329996 9330441 4.030000e-136 496.0
38 TraesCS4A01G467600 chr7A 88.889 54 3 3 5516 5566 483946129 483946076 4.840000e-06 63.9
39 TraesCS4A01G467600 chr7D 87.594 2128 224 23 2786 4890 10471140 10469030 0.000000e+00 2431.0
40 TraesCS4A01G467600 chr7D 88.849 1937 193 13 2753 4682 10479395 10477475 0.000000e+00 2359.0
41 TraesCS4A01G467600 chr7D 87.303 1331 141 15 1152 2461 10480941 10479618 0.000000e+00 1496.0
42 TraesCS4A01G467600 chr7D 83.896 1155 151 18 1333 2462 10037243 10038387 0.000000e+00 1070.0
43 TraesCS4A01G467600 chr7D 89.725 837 73 8 2788 3622 10038657 10039482 0.000000e+00 1057.0
44 TraesCS4A01G467600 chr7D 84.971 692 60 21 476 1139 10481599 10480924 0.000000e+00 662.0
45 TraesCS4A01G467600 chr7D 86.111 468 49 13 1 457 10482126 10481664 1.870000e-134 490.0
46 TraesCS4A01G467600 chr7D 85.558 457 57 8 2 455 10036419 10036869 2.440000e-128 470.0
47 TraesCS4A01G467600 chr7D 81.877 309 49 5 583 891 10472737 10472436 2.680000e-63 254.0
48 TraesCS4A01G467600 chr7D 89.231 130 8 5 5557 5685 10468675 10468551 2.160000e-34 158.0
49 TraesCS4A01G467600 chr7D 91.304 46 4 0 5512 5557 312564479 312564524 4.840000e-06 63.9
50 TraesCS4A01G467600 chr7D 91.111 45 3 1 5516 5559 5041207 5041163 6.270000e-05 60.2
51 TraesCS4A01G467600 chr1D 74.153 1888 388 73 2836 4674 488484227 488486063 0.000000e+00 691.0
52 TraesCS4A01G467600 chr1D 95.679 162 6 1 2463 2624 246429889 246429729 5.760000e-65 259.0
53 TraesCS4A01G467600 chrUn 95.679 162 6 1 2463 2624 430359087 430358927 5.760000e-65 259.0
54 TraesCS4A01G467600 chr6B 96.795 156 4 1 2463 2618 18748358 18748512 5.760000e-65 259.0
55 TraesCS4A01G467600 chr5D 96.795 156 4 1 2463 2618 6264245 6264399 5.760000e-65 259.0
56 TraesCS4A01G467600 chr5D 96.795 156 3 2 2463 2618 329152156 329152309 5.760000e-65 259.0
57 TraesCS4A01G467600 chr5D 95.679 162 6 1 2463 2624 503303567 503303407 5.760000e-65 259.0
58 TraesCS4A01G467600 chr3D 89.796 49 5 0 5512 5560 324311121 324311169 4.840000e-06 63.9
59 TraesCS4A01G467600 chr3A 89.796 49 5 0 5512 5560 397141416 397141368 4.840000e-06 63.9
60 TraesCS4A01G467600 chr2A 91.304 46 4 0 5516 5561 570013462 570013507 4.840000e-06 63.9
61 TraesCS4A01G467600 chr2D 91.111 45 4 0 5512 5556 159688989 159688945 1.740000e-05 62.1
62 TraesCS4A01G467600 chr5B 87.755 49 5 1 5512 5559 478522773 478522821 8.100000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G467600 chr4A 729682455 729688244 5789 False 3661.000000 10693 88.257333 1 5790 3 chr4A.!!$F4 5789
1 TraesCS4A01G467600 chr4A 718925603 718929875 4272 True 5419.000000 5419 89.754000 457 4703 1 chr4A.!!$R1 4246
2 TraesCS4A01G467600 chr4A 729077671 729084742 7071 True 1731.000000 3391 89.766667 1170 5681 3 chr4A.!!$R5 4511
3 TraesCS4A01G467600 chr4A 729530351 729532843 2492 True 1481.500000 2296 90.405500 1 2423 2 chr4A.!!$R6 2422
4 TraesCS4A01G467600 chr4A 729147705 729149281 1576 False 1478.000000 1478 83.760000 3092 4674 1 chr4A.!!$F2 1582
5 TraesCS4A01G467600 chr4A 728829348 728833443 4095 False 1266.000000 2394 87.636333 1170 4890 3 chr4A.!!$F3 3720
6 TraesCS4A01G467600 chr4A 729859063 729864325 5262 False 1165.200000 2473 87.245200 20 5515 5 chr4A.!!$F7 5495
7 TraesCS4A01G467600 chr4A 729743810 729747964 4154 False 1148.500000 1899 83.877000 3 4674 2 chr4A.!!$F5 4671
8 TraesCS4A01G467600 chr4A 728425783 728432475 6692 True 931.285714 2743 89.507000 18 5623 7 chr4A.!!$R3 5605
9 TraesCS4A01G467600 chr4A 729047368 729048776 1408 True 833.500000 1365 91.056500 456 1892 2 chr4A.!!$R4 1436
10 TraesCS4A01G467600 chr4A 729814993 729815755 762 False 433.500000 484 89.181500 18 730 2 chr4A.!!$F6 712
11 TraesCS4A01G467600 chr7A 9329996 9335763 5767 False 2081.333333 4737 87.113667 18 5066 3 chr7A.!!$F1 5048
12 TraesCS4A01G467600 chr7D 10477475 10482126 4651 True 1251.750000 2359 86.808500 1 4682 4 chr7D.!!$R3 4681
13 TraesCS4A01G467600 chr7D 10468551 10472737 4186 True 947.666667 2431 86.234000 583 5685 3 chr7D.!!$R2 5102
14 TraesCS4A01G467600 chr7D 10036419 10039482 3063 False 865.666667 1070 86.393000 2 3622 3 chr7D.!!$F2 3620
15 TraesCS4A01G467600 chr1D 488484227 488486063 1836 False 691.000000 691 74.153000 2836 4674 1 chr1D.!!$F1 1838

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
984 1101 0.179108 GTGGCGTCTAGGGTGATGAC 60.179 60.000 0.00 0.00 0.00 3.06 F
1506 1630 1.625818 GCCAACAGAAGAAGAGGAGGA 59.374 52.381 0.00 0.00 0.00 3.71 F
2486 5364 0.676782 CTTTTGCCTGGGTACTCGGG 60.677 60.000 17.12 17.12 36.28 5.14 F
4064 8053 0.105593 ATCATTGCGGACTCTGCGAT 59.894 50.000 6.76 6.76 36.90 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1927 0.250467 GTGAAGTTCAGCAGCCTCCA 60.250 55.0 5.62 0.0 0.00 3.86 R
3004 6271 0.449786 TCATTGTGTAAATGCGCCCG 59.550 50.0 4.18 0.0 0.00 6.13 R
4236 8243 0.299895 CTCACGCTCAACATGATCGC 59.700 55.0 0.00 0.0 39.34 4.58 R
5755 11118 0.031716 TGCTCTAGGAGGTGCCATCT 60.032 55.0 0.00 0.0 40.02 2.90 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 270 7.552330 ACATGTTTAGCAGAAACCACAATTTTT 59.448 29.630 10.66 0.00 0.00 1.94
289 300 6.405397 GGAAAAAGTGCAACCCGTATATTCAT 60.405 38.462 0.00 0.00 37.80 2.57
372 383 9.083422 TGTAATGATCTTCCACACCAAAAATAA 57.917 29.630 0.00 0.00 0.00 1.40
373 384 9.921637 GTAATGATCTTCCACACCAAAAATAAA 57.078 29.630 0.00 0.00 0.00 1.40
696 789 1.563879 TGGAATACTGGGTGATGTGGG 59.436 52.381 0.00 0.00 0.00 4.61
719 812 6.868339 GGGAATTTCAAATTGGTCTGTTACAG 59.132 38.462 5.94 5.94 0.00 2.74
752 845 1.561542 CCTCAACAGAAGGGCAGGTAT 59.438 52.381 0.00 0.00 0.00 2.73
896 992 3.719268 TGGATGGTTCTGCTGTTACAT 57.281 42.857 0.00 0.00 0.00 2.29
897 993 4.032960 TGGATGGTTCTGCTGTTACATT 57.967 40.909 0.00 0.00 0.00 2.71
898 994 3.758023 TGGATGGTTCTGCTGTTACATTG 59.242 43.478 0.00 0.00 0.00 2.82
899 995 3.129287 GGATGGTTCTGCTGTTACATTGG 59.871 47.826 0.00 0.00 0.00 3.16
900 996 3.500448 TGGTTCTGCTGTTACATTGGA 57.500 42.857 0.00 0.00 0.00 3.53
904 1000 3.610040 TCTGCTGTTACATTGGACGAT 57.390 42.857 0.00 0.00 0.00 3.73
905 1001 3.261580 TCTGCTGTTACATTGGACGATG 58.738 45.455 0.00 0.00 0.00 3.84
906 1002 2.352651 CTGCTGTTACATTGGACGATGG 59.647 50.000 4.67 0.00 0.00 3.51
907 1003 1.064060 GCTGTTACATTGGACGATGGC 59.936 52.381 4.67 0.00 0.00 4.40
908 1004 2.355197 CTGTTACATTGGACGATGGCA 58.645 47.619 4.67 0.00 0.00 4.92
909 1005 2.746904 CTGTTACATTGGACGATGGCAA 59.253 45.455 0.00 0.00 0.00 4.52
911 1007 3.761218 TGTTACATTGGACGATGGCAAAT 59.239 39.130 0.00 0.00 0.00 2.32
912 1008 4.219507 TGTTACATTGGACGATGGCAAATT 59.780 37.500 0.00 0.00 0.00 1.82
971 1088 1.536766 CATCAAACATGAGTGTGGCGT 59.463 47.619 0.00 0.00 38.92 5.68
978 1095 0.614979 ATGAGTGTGGCGTCTAGGGT 60.615 55.000 0.00 0.00 0.00 4.34
979 1096 1.215647 GAGTGTGGCGTCTAGGGTG 59.784 63.158 0.00 0.00 0.00 4.61
980 1097 1.228769 AGTGTGGCGTCTAGGGTGA 60.229 57.895 0.00 0.00 0.00 4.02
981 1098 0.614979 AGTGTGGCGTCTAGGGTGAT 60.615 55.000 0.00 0.00 0.00 3.06
982 1099 0.460284 GTGTGGCGTCTAGGGTGATG 60.460 60.000 0.00 0.00 0.00 3.07
983 1100 0.613572 TGTGGCGTCTAGGGTGATGA 60.614 55.000 0.00 0.00 0.00 2.92
984 1101 0.179108 GTGGCGTCTAGGGTGATGAC 60.179 60.000 0.00 0.00 0.00 3.06
1024 1141 2.422597 CAAGCTTACCACGTTCATGGA 58.577 47.619 0.00 0.00 43.02 3.41
1041 1161 4.156373 TCATGGACAACGAGTACAATACGA 59.844 41.667 2.04 0.00 46.24 3.43
1126 1246 2.625737 CGGATGAGCTGAAGTTGATGT 58.374 47.619 0.00 0.00 0.00 3.06
1146 1266 3.257375 TGTGTAATTCTGTCGCTAGTGGT 59.743 43.478 2.90 0.00 0.00 4.16
1147 1267 3.612860 GTGTAATTCTGTCGCTAGTGGTG 59.387 47.826 2.90 0.00 0.00 4.17
1196 1316 2.268076 AACTGCAACCATCGGCACC 61.268 57.895 0.00 0.00 35.86 5.01
1254 1374 4.464008 AGAACAAGAGAAAGGCATCAACA 58.536 39.130 0.00 0.00 0.00 3.33
1506 1630 1.625818 GCCAACAGAAGAAGAGGAGGA 59.374 52.381 0.00 0.00 0.00 3.71
1760 1886 7.162761 TGGAAAATTGCATTGATGACTTCATT 58.837 30.769 0.00 0.00 36.57 2.57
1791 1917 2.127708 GGGGTGAGGATGTTGAGGTAT 58.872 52.381 0.00 0.00 0.00 2.73
1801 1927 6.012745 AGGATGTTGAGGTATGCTTTTTCTT 58.987 36.000 0.00 0.00 0.00 2.52
1838 1964 0.679505 ACAAGAGGTTGTGCGAGCTA 59.320 50.000 0.00 0.00 45.58 3.32
2010 2136 0.901580 CCTTGTGGGCATTGAAGGCT 60.902 55.000 0.72 0.00 0.00 4.58
2048 2174 8.946085 GTTATCAGTTGGTTGATGAATACTCAA 58.054 33.333 0.00 0.00 38.25 3.02
2227 2353 7.492344 CCTACAATTGAAACTTGGGATAAATGC 59.508 37.037 13.59 0.00 0.00 3.56
2351 5221 5.932303 TGAAGTAGCAAGTAATTGGTCAGTC 59.068 40.000 11.30 7.69 34.21 3.51
2353 5223 4.532521 AGTAGCAAGTAATTGGTCAGTCCT 59.467 41.667 11.30 0.00 37.07 3.85
2360 5230 5.552178 AGTAATTGGTCAGTCCTTGTTCTC 58.448 41.667 0.00 0.00 37.07 2.87
2475 5353 1.959282 CAGAAACTCTGCCTTTTGCCT 59.041 47.619 0.00 0.00 37.72 4.75
2486 5364 0.676782 CTTTTGCCTGGGTACTCGGG 60.677 60.000 17.12 17.12 36.28 5.14
2495 5373 3.054948 CCTGGGTACTCGGGTTCAAATAA 60.055 47.826 13.03 0.00 0.00 1.40
2497 5375 3.273434 GGGTACTCGGGTTCAAATAACC 58.727 50.000 0.00 0.00 39.56 2.85
2620 5498 4.640771 TGTTTCTTTAGCAGATCCCACT 57.359 40.909 0.00 0.00 0.00 4.00
2659 5538 9.850628 GGGAAAAACTGATTTAAGTATTGTACC 57.149 33.333 0.00 0.00 0.00 3.34
2719 5602 0.787084 AGAGTCTTGTGAGGGAGGGA 59.213 55.000 0.00 0.00 0.00 4.20
2733 5997 4.890306 GGGAGGGAGGGAGGGAGC 62.890 77.778 0.00 0.00 0.00 4.70
2762 6027 3.873952 GACCAACCATCAGAGCAATAGAC 59.126 47.826 0.00 0.00 0.00 2.59
3004 6271 2.690778 GGCCTGTCACAATGACCGC 61.691 63.158 6.51 7.79 46.40 5.68
3006 6273 2.390599 CCTGTCACAATGACCGCGG 61.391 63.158 26.86 26.86 46.40 6.46
3008 6275 3.799755 GTCACAATGACCGCGGGC 61.800 66.667 31.76 30.24 41.37 6.13
3301 6568 3.914426 AACCTTAGCTACACCCATCTG 57.086 47.619 0.00 0.00 0.00 2.90
3486 6753 8.566260 GCTTATCAATAGAAACATGATTCAGCT 58.434 33.333 16.93 0.51 36.59 4.24
3755 7037 5.297527 TCATTACTGTTCGAGGACGCTATAA 59.702 40.000 0.00 0.00 39.58 0.98
3872 7175 5.953571 TGAGGTATCTGATGGTTAGAGCTA 58.046 41.667 0.00 0.00 0.00 3.32
3925 7914 5.069914 TGAGCTTGTTTACTTGGAGACACTA 59.930 40.000 0.00 0.00 42.67 2.74
3942 7931 7.201565 GGAGACACTAGACATAGAAAATTGCAC 60.202 40.741 0.00 0.00 32.93 4.57
4007 7996 3.390639 CCTGTCCTATCTGCTTCTTCCAT 59.609 47.826 0.00 0.00 0.00 3.41
4033 8022 3.191371 GGACAAAGTTGCCTGAAGGTATG 59.809 47.826 0.00 0.00 37.57 2.39
4034 8023 4.072131 GACAAAGTTGCCTGAAGGTATGA 58.928 43.478 0.00 0.00 37.57 2.15
4035 8024 4.666512 ACAAAGTTGCCTGAAGGTATGAT 58.333 39.130 0.00 0.00 37.57 2.45
4064 8053 0.105593 ATCATTGCGGACTCTGCGAT 59.894 50.000 6.76 6.76 36.90 4.58
4236 8243 0.250234 TCTCTGGTCATCTTTGGCGG 59.750 55.000 0.00 0.00 0.00 6.13
4238 8245 2.745884 TGGTCATCTTTGGCGGCG 60.746 61.111 0.51 0.51 0.00 6.46
4258 8265 1.929836 GATCATGTTGAGCGTGAGGAC 59.070 52.381 0.00 0.00 45.30 3.85
4353 8360 4.937201 GGAGAGTTCCAAAATGGTTGTT 57.063 40.909 0.00 0.00 43.45 2.83
4361 8368 4.399004 CCAAAATGGTTGTTTGGTCTCA 57.601 40.909 7.60 0.00 46.64 3.27
4464 8471 2.094675 CCACCTCGAATTTGGAGCATT 58.905 47.619 3.10 0.00 31.39 3.56
4478 8485 2.833943 GGAGCATTTGAAATCCCTGGTT 59.166 45.455 0.00 0.00 0.00 3.67
4480 8487 4.142160 GGAGCATTTGAAATCCCTGGTTAC 60.142 45.833 0.00 0.00 0.00 2.50
4495 8502 3.950397 TGGTTACAGAGCTATGTTTGGG 58.050 45.455 20.67 0.00 34.56 4.12
4682 8692 2.702478 CTCCAGGAGATCCAAGTGCATA 59.298 50.000 11.62 0.00 38.89 3.14
4685 8695 1.202580 AGGAGATCCAAGTGCATACGC 60.203 52.381 0.92 0.00 38.89 4.42
4689 8699 2.959030 AGATCCAAGTGCATACGCTCTA 59.041 45.455 0.00 0.00 41.01 2.43
4705 8715 6.710597 ACGCTCTACATTAGTAAGGATTCA 57.289 37.500 0.75 0.00 0.00 2.57
4718 8728 1.168714 GGATTCAGTGGACAGGTTGC 58.831 55.000 0.00 0.00 0.00 4.17
4845 8865 3.069586 TGTCTATCTTTCATACCCCTGCG 59.930 47.826 0.00 0.00 0.00 5.18
4881 8902 1.147153 AGCTGATTAAGGCGCTCCC 59.853 57.895 7.64 0.00 0.00 4.30
4890 8911 0.179081 AAGGCGCTCCCGATCTTTAC 60.179 55.000 7.64 0.00 39.21 2.01
4891 8912 1.594564 GGCGCTCCCGATCTTTACC 60.595 63.158 7.64 0.00 36.29 2.85
4893 8914 0.876342 GCGCTCCCGATCTTTACCTG 60.876 60.000 0.00 0.00 36.29 4.00
4899 8920 1.470979 CCCGATCTTTACCTGTGTCCG 60.471 57.143 0.00 0.00 0.00 4.79
4901 8922 1.135083 CGATCTTTACCTGTGTCCGCT 60.135 52.381 0.00 0.00 0.00 5.52
4902 8923 2.271800 GATCTTTACCTGTGTCCGCTG 58.728 52.381 0.00 0.00 0.00 5.18
4903 8924 0.320374 TCTTTACCTGTGTCCGCTGG 59.680 55.000 2.61 2.61 0.00 4.85
4904 8925 0.320374 CTTTACCTGTGTCCGCTGGA 59.680 55.000 10.29 0.00 0.00 3.86
4905 8926 0.981183 TTTACCTGTGTCCGCTGGAT 59.019 50.000 10.29 0.00 32.73 3.41
4906 8927 0.535335 TTACCTGTGTCCGCTGGATC 59.465 55.000 10.29 0.00 32.73 3.36
4907 8928 0.613572 TACCTGTGTCCGCTGGATCA 60.614 55.000 10.29 3.79 32.73 2.92
4908 8929 1.296392 CCTGTGTCCGCTGGATCAA 59.704 57.895 0.00 0.00 32.73 2.57
4909 8930 0.742281 CCTGTGTCCGCTGGATCAAG 60.742 60.000 0.00 0.00 32.73 3.02
4940 9117 4.016444 CCTAATGTGGTTGTACTGCCAAT 58.984 43.478 9.89 5.01 36.41 3.16
4948 9125 2.884639 GTTGTACTGCCAATTGTGTCCT 59.115 45.455 4.43 0.00 0.00 3.85
4979 9160 3.838565 TGTTTTTGACAGCTAATGGGGA 58.161 40.909 0.00 0.00 33.40 4.81
4996 9177 6.731639 ATGGGGATTATGGATCAAGATCTT 57.268 37.500 0.88 0.88 37.92 2.40
4998 9179 6.309357 TGGGGATTATGGATCAAGATCTTTG 58.691 40.000 4.86 1.96 37.92 2.77
5026 9207 5.967088 TCTTGTAATCTGCCTCTCTGTAAC 58.033 41.667 0.00 0.00 0.00 2.50
5094 9286 7.500559 CCTGAAAAAGGTAATCCTAGGATTCAG 59.499 40.741 35.17 30.14 44.35 3.02
5100 9355 1.811778 ATCCTAGGATTCAGGCTGCA 58.188 50.000 19.18 0.00 32.82 4.41
5112 9367 2.040278 TCAGGCTGCATTTGGTCTAGTT 59.960 45.455 10.34 0.00 0.00 2.24
5132 9401 9.426534 TCTAGTTATACTTAACCTAAACCCCTC 57.573 37.037 0.00 0.00 38.81 4.30
5137 9406 0.614812 TAACCTAAACCCCTCGGTGC 59.385 55.000 0.00 0.00 43.71 5.01
5138 9407 2.125269 CCTAAACCCCTCGGTGCG 60.125 66.667 0.00 0.00 43.71 5.34
5162 9431 6.579865 GGTGCTAATTGCTAGGTTAAGTAGA 58.420 40.000 0.00 0.00 43.37 2.59
5170 9440 9.601217 AATTGCTAGGTTAAGTAGATAACACTG 57.399 33.333 0.00 0.00 37.48 3.66
5174 9444 7.854916 GCTAGGTTAAGTAGATAACACTGTACG 59.145 40.741 0.00 0.00 37.48 3.67
5175 9445 6.558909 AGGTTAAGTAGATAACACTGTACGC 58.441 40.000 0.00 0.00 37.48 4.42
5283 9806 9.638239 TTTCAATTGCATACAACCTTCTAATTC 57.362 29.630 0.00 0.00 38.99 2.17
5318 9841 5.006358 ACGTATCGTGTTAATTGCTGGATTC 59.994 40.000 0.00 0.00 39.18 2.52
5325 9848 4.158394 TGTTAATTGCTGGATTCAGGCTTC 59.842 41.667 2.40 0.00 41.19 3.86
5329 9852 2.811410 TGCTGGATTCAGGCTTCATTT 58.189 42.857 2.40 0.00 41.19 2.32
5339 9862 5.789643 TCAGGCTTCATTTTTGCTTACTT 57.210 34.783 0.00 0.00 0.00 2.24
5380 10742 0.485099 TGTTAATTGCTGGGTGGGGT 59.515 50.000 0.00 0.00 0.00 4.95
5381 10743 1.711375 TGTTAATTGCTGGGTGGGGTA 59.289 47.619 0.00 0.00 0.00 3.69
5382 10744 2.291282 TGTTAATTGCTGGGTGGGGTAG 60.291 50.000 0.00 0.00 0.00 3.18
5383 10745 1.676248 TAATTGCTGGGTGGGGTAGT 58.324 50.000 0.00 0.00 0.00 2.73
5384 10746 0.331616 AATTGCTGGGTGGGGTAGTC 59.668 55.000 0.00 0.00 0.00 2.59
5388 10751 1.774894 GCTGGGTGGGGTAGTCAACA 61.775 60.000 0.00 0.00 0.00 3.33
5412 10775 7.041372 ACACTTTTAAGCCTGTGTACATAAGTG 60.041 37.037 12.49 12.49 41.17 3.16
5479 10842 9.535270 GAATCTTTATTCTCTCGTGTTTTCAAG 57.465 33.333 0.00 0.00 38.79 3.02
5520 10883 5.210715 GTCAAGTGAAAGATTGTCAGCTTG 58.789 41.667 0.00 0.00 36.51 4.01
5521 10884 4.276678 TCAAGTGAAAGATTGTCAGCTTGG 59.723 41.667 0.00 0.00 36.22 3.61
5630 10993 5.302823 AGCTTTGCCTTATTCTGAAGTGTTT 59.697 36.000 0.00 0.00 0.00 2.83
5632 10995 6.582672 GCTTTGCCTTATTCTGAAGTGTTTAC 59.417 38.462 0.00 0.00 0.00 2.01
5636 10999 8.856153 TGCCTTATTCTGAAGTGTTTACAATA 57.144 30.769 0.00 0.00 0.00 1.90
5685 11048 0.027979 CCGACTGTGTGCAAACTGTG 59.972 55.000 22.76 14.47 32.99 3.66
5686 11049 0.726827 CGACTGTGTGCAAACTGTGT 59.273 50.000 22.76 11.70 32.99 3.72
5687 11050 1.267532 CGACTGTGTGCAAACTGTGTC 60.268 52.381 22.76 17.78 32.99 3.67
5688 11051 2.009774 GACTGTGTGCAAACTGTGTCT 58.990 47.619 22.76 0.00 32.99 3.41
5689 11052 1.739466 ACTGTGTGCAAACTGTGTCTG 59.261 47.619 17.85 0.00 31.80 3.51
5690 11053 1.739466 CTGTGTGCAAACTGTGTCTGT 59.261 47.619 8.83 0.00 0.00 3.41
5691 11054 1.468127 TGTGTGCAAACTGTGTCTGTG 59.532 47.619 8.83 0.00 0.00 3.66
5692 11055 1.737236 GTGTGCAAACTGTGTCTGTGA 59.263 47.619 0.00 0.00 0.00 3.58
5693 11056 2.161410 GTGTGCAAACTGTGTCTGTGAA 59.839 45.455 0.00 0.00 0.00 3.18
5694 11057 2.161410 TGTGCAAACTGTGTCTGTGAAC 59.839 45.455 0.00 0.00 0.00 3.18
5695 11058 1.742831 TGCAAACTGTGTCTGTGAACC 59.257 47.619 0.00 0.00 0.00 3.62
5696 11059 2.017049 GCAAACTGTGTCTGTGAACCT 58.983 47.619 0.00 0.00 0.00 3.50
5697 11060 2.423538 GCAAACTGTGTCTGTGAACCTT 59.576 45.455 0.00 0.00 0.00 3.50
5698 11061 3.625764 GCAAACTGTGTCTGTGAACCTTA 59.374 43.478 0.00 0.00 0.00 2.69
5699 11062 4.095782 GCAAACTGTGTCTGTGAACCTTAA 59.904 41.667 0.00 0.00 0.00 1.85
5700 11063 5.569413 CAAACTGTGTCTGTGAACCTTAAC 58.431 41.667 0.00 0.00 0.00 2.01
5701 11064 4.755266 ACTGTGTCTGTGAACCTTAACT 57.245 40.909 0.00 0.00 0.00 2.24
5702 11065 4.442706 ACTGTGTCTGTGAACCTTAACTG 58.557 43.478 0.00 0.00 0.00 3.16
5703 11066 4.081087 ACTGTGTCTGTGAACCTTAACTGT 60.081 41.667 0.00 0.00 0.00 3.55
5704 11067 4.439057 TGTGTCTGTGAACCTTAACTGTC 58.561 43.478 0.00 0.00 0.00 3.51
5705 11068 4.081365 TGTGTCTGTGAACCTTAACTGTCA 60.081 41.667 0.00 0.00 0.00 3.58
5706 11069 5.057149 GTGTCTGTGAACCTTAACTGTCAT 58.943 41.667 0.00 0.00 0.00 3.06
5707 11070 5.527582 GTGTCTGTGAACCTTAACTGTCATT 59.472 40.000 0.00 0.00 0.00 2.57
5708 11071 6.038271 GTGTCTGTGAACCTTAACTGTCATTT 59.962 38.462 0.00 0.00 0.00 2.32
5709 11072 6.038161 TGTCTGTGAACCTTAACTGTCATTTG 59.962 38.462 0.00 0.00 0.00 2.32
5710 11073 6.038271 GTCTGTGAACCTTAACTGTCATTTGT 59.962 38.462 0.00 0.00 0.00 2.83
5711 11074 6.601613 TCTGTGAACCTTAACTGTCATTTGTT 59.398 34.615 0.00 0.00 0.00 2.83
5712 11075 6.559810 TGTGAACCTTAACTGTCATTTGTTG 58.440 36.000 0.00 0.00 0.00 3.33
5713 11076 5.977129 GTGAACCTTAACTGTCATTTGTTGG 59.023 40.000 0.00 0.00 0.00 3.77
5714 11077 5.888724 TGAACCTTAACTGTCATTTGTTGGA 59.111 36.000 0.00 0.00 0.00 3.53
5715 11078 6.378564 TGAACCTTAACTGTCATTTGTTGGAA 59.621 34.615 0.00 0.00 0.00 3.53
5716 11079 6.144078 ACCTTAACTGTCATTTGTTGGAAC 57.856 37.500 0.00 0.00 0.00 3.62
5717 11080 5.654650 ACCTTAACTGTCATTTGTTGGAACA 59.345 36.000 0.00 0.00 37.08 3.18
5730 11093 1.993956 TGGAACAACCAAGTCCATGG 58.006 50.000 4.97 4.97 46.75 3.66
5731 11094 0.603065 GGAACAACCAAGTCCATGGC 59.397 55.000 6.96 2.00 44.75 4.40
5732 11095 1.327303 GAACAACCAAGTCCATGGCA 58.673 50.000 6.96 0.00 44.75 4.92
5733 11096 1.686052 GAACAACCAAGTCCATGGCAA 59.314 47.619 6.96 0.00 44.75 4.52
5734 11097 1.786937 ACAACCAAGTCCATGGCAAA 58.213 45.000 6.96 0.00 44.75 3.68
5735 11098 1.688197 ACAACCAAGTCCATGGCAAAG 59.312 47.619 6.96 0.00 44.75 2.77
5736 11099 1.001181 CAACCAAGTCCATGGCAAAGG 59.999 52.381 6.96 9.15 44.75 3.11
5737 11100 1.187567 ACCAAGTCCATGGCAAAGGC 61.188 55.000 6.96 0.00 44.75 4.35
5738 11101 0.901580 CCAAGTCCATGGCAAAGGCT 60.902 55.000 6.96 0.00 40.87 4.58
5739 11102 1.616725 CCAAGTCCATGGCAAAGGCTA 60.617 52.381 6.96 0.00 40.87 3.93
5740 11103 2.381911 CAAGTCCATGGCAAAGGCTAT 58.618 47.619 6.96 0.00 42.59 2.97
5741 11104 2.355010 AGTCCATGGCAAAGGCTATC 57.645 50.000 6.96 0.00 39.46 2.08
5742 11105 1.849039 AGTCCATGGCAAAGGCTATCT 59.151 47.619 6.96 0.00 39.46 1.98
5743 11106 2.158696 AGTCCATGGCAAAGGCTATCTC 60.159 50.000 6.96 0.00 39.46 2.75
5744 11107 1.143684 TCCATGGCAAAGGCTATCTCC 59.856 52.381 6.96 0.00 39.46 3.71
5745 11108 1.144503 CCATGGCAAAGGCTATCTCCT 59.855 52.381 0.00 0.00 39.46 3.69
5746 11109 2.373169 CCATGGCAAAGGCTATCTCCTA 59.627 50.000 0.00 0.00 39.46 2.94
5747 11110 3.009916 CCATGGCAAAGGCTATCTCCTAT 59.990 47.826 0.00 0.00 39.46 2.57
5748 11111 3.777106 TGGCAAAGGCTATCTCCTATG 57.223 47.619 0.00 0.00 40.87 2.23
5749 11112 2.224621 TGGCAAAGGCTATCTCCTATGC 60.225 50.000 0.00 0.00 40.87 3.14
5750 11113 2.224621 GGCAAAGGCTATCTCCTATGCA 60.225 50.000 0.00 0.00 40.87 3.96
5751 11114 3.072944 GCAAAGGCTATCTCCTATGCAG 58.927 50.000 0.00 0.00 34.82 4.41
5752 11115 3.672808 CAAAGGCTATCTCCTATGCAGG 58.327 50.000 0.00 0.00 44.17 4.85
5753 11116 1.949799 AGGCTATCTCCTATGCAGGG 58.050 55.000 0.00 0.00 42.87 4.45
5754 11117 0.908198 GGCTATCTCCTATGCAGGGG 59.092 60.000 8.39 5.18 44.91 4.79
5760 11123 0.982704 CTCCTATGCAGGGGAGATGG 59.017 60.000 24.96 6.22 46.77 3.51
5761 11124 1.130054 TCCTATGCAGGGGAGATGGC 61.130 60.000 6.36 0.00 42.87 4.40
5762 11125 1.421346 CCTATGCAGGGGAGATGGCA 61.421 60.000 1.90 0.00 38.41 4.92
5763 11126 0.250640 CTATGCAGGGGAGATGGCAC 60.251 60.000 0.00 0.00 39.34 5.01
5764 11127 1.708993 TATGCAGGGGAGATGGCACC 61.709 60.000 0.00 0.00 39.34 5.01
5765 11128 3.415087 GCAGGGGAGATGGCACCT 61.415 66.667 0.00 0.00 0.00 4.00
5766 11129 2.914289 CAGGGGAGATGGCACCTC 59.086 66.667 0.00 0.00 0.00 3.85
5771 11134 3.541224 GGAGATGGCACCTCCTAGA 57.459 57.895 21.35 0.00 45.18 2.43
5772 11135 1.337118 GGAGATGGCACCTCCTAGAG 58.663 60.000 21.35 0.00 45.18 2.43
5773 11136 0.678950 GAGATGGCACCTCCTAGAGC 59.321 60.000 0.00 0.00 35.26 4.09
5774 11137 0.031716 AGATGGCACCTCCTAGAGCA 60.032 55.000 0.00 0.00 35.26 4.26
5775 11138 0.392336 GATGGCACCTCCTAGAGCAG 59.608 60.000 0.00 0.00 35.26 4.24
5776 11139 0.031716 ATGGCACCTCCTAGAGCAGA 60.032 55.000 0.00 0.00 35.26 4.26
5777 11140 0.685785 TGGCACCTCCTAGAGCAGAG 60.686 60.000 0.00 0.00 35.26 3.35
5778 11141 1.441311 GCACCTCCTAGAGCAGAGC 59.559 63.158 0.00 0.00 0.00 4.09
5779 11142 1.326213 GCACCTCCTAGAGCAGAGCA 61.326 60.000 0.00 0.00 0.00 4.26
5780 11143 0.746063 CACCTCCTAGAGCAGAGCAG 59.254 60.000 0.00 0.00 0.00 4.24
5781 11144 0.396974 ACCTCCTAGAGCAGAGCAGG 60.397 60.000 0.00 0.00 0.00 4.85
5782 11145 0.396974 CCTCCTAGAGCAGAGCAGGT 60.397 60.000 0.00 0.00 0.00 4.00
5783 11146 0.746063 CTCCTAGAGCAGAGCAGGTG 59.254 60.000 0.00 0.00 0.00 4.00
5784 11147 0.685785 TCCTAGAGCAGAGCAGGTGG 60.686 60.000 0.00 0.00 0.00 4.61
5785 11148 1.143620 CTAGAGCAGAGCAGGTGGC 59.856 63.158 0.00 0.00 45.30 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 222 9.057089 GCTAAACATGTTATCTATAGTGGCTTT 57.943 33.333 12.39 0.00 0.00 3.51
232 242 6.701145 TTGTGGTTTCTGCTAAACATGTTA 57.299 33.333 12.39 0.00 32.04 2.41
260 270 1.134670 CGGGTTGCACTTTTTCCCAAA 60.135 47.619 0.00 0.00 38.15 3.28
265 276 5.945155 TGAATATACGGGTTGCACTTTTTC 58.055 37.500 0.00 0.00 0.00 2.29
311 322 7.424227 TCAAATCTTGTCATTTGCAAATTCC 57.576 32.000 21.95 14.97 41.65 3.01
480 547 9.584008 AAGAAGGATGACATGCATTTAGAATAT 57.416 29.630 9.80 0.00 37.34 1.28
696 789 7.382218 CACCTGTAACAGACCAATTTGAAATTC 59.618 37.037 0.00 0.00 32.44 2.17
719 812 3.767673 TCTGTTGAGGTACCTACATCACC 59.232 47.826 16.29 1.63 45.27 4.02
792 885 2.571202 TGGCCATGACACATCACTAGAA 59.429 45.455 0.00 0.00 37.79 2.10
822 916 6.348704 GGCAATGCTTATCTGCAACAAAAATT 60.349 34.615 4.82 0.00 46.61 1.82
896 992 1.543802 GTCCAATTTGCCATCGTCCAA 59.456 47.619 0.00 0.00 0.00 3.53
897 993 1.173043 GTCCAATTTGCCATCGTCCA 58.827 50.000 0.00 0.00 0.00 4.02
898 994 0.098728 CGTCCAATTTGCCATCGTCC 59.901 55.000 0.00 0.00 0.00 4.79
899 995 1.083489 TCGTCCAATTTGCCATCGTC 58.917 50.000 0.00 0.00 0.00 4.20
900 996 1.401552 CATCGTCCAATTTGCCATCGT 59.598 47.619 0.00 0.00 0.00 3.73
904 1000 0.897401 TGCCATCGTCCAATTTGCCA 60.897 50.000 0.00 0.00 0.00 4.92
905 1001 0.246086 TTGCCATCGTCCAATTTGCC 59.754 50.000 0.00 0.00 0.00 4.52
906 1002 2.077413 TTTGCCATCGTCCAATTTGC 57.923 45.000 0.00 0.00 0.00 3.68
907 1003 4.244066 TCAATTTGCCATCGTCCAATTTG 58.756 39.130 0.00 0.00 35.37 2.32
908 1004 4.497300 CTCAATTTGCCATCGTCCAATTT 58.503 39.130 0.00 0.00 0.00 1.82
909 1005 3.676873 GCTCAATTTGCCATCGTCCAATT 60.677 43.478 0.00 0.00 0.00 2.32
911 1007 1.202114 GCTCAATTTGCCATCGTCCAA 59.798 47.619 0.00 0.00 0.00 3.53
912 1008 0.810648 GCTCAATTTGCCATCGTCCA 59.189 50.000 0.00 0.00 0.00 4.02
971 1088 2.961741 GCTCATCAGTCATCACCCTAGA 59.038 50.000 0.00 0.00 0.00 2.43
978 1095 2.367894 GGAGGATGCTCATCAGTCATCA 59.632 50.000 16.72 0.00 39.54 3.07
979 1096 2.367894 TGGAGGATGCTCATCAGTCATC 59.632 50.000 16.72 0.00 39.54 2.92
980 1097 2.405559 TGGAGGATGCTCATCAGTCAT 58.594 47.619 16.72 0.00 39.54 3.06
981 1098 1.870064 TGGAGGATGCTCATCAGTCA 58.130 50.000 16.72 0.47 39.54 3.41
982 1099 2.550423 CCATGGAGGATGCTCATCAGTC 60.550 54.545 16.72 7.35 41.22 3.51
983 1100 1.420514 CCATGGAGGATGCTCATCAGT 59.579 52.381 16.72 0.00 41.22 3.41
984 1101 1.882780 GCCATGGAGGATGCTCATCAG 60.883 57.143 18.40 3.10 41.22 2.90
1024 1141 9.282247 CTAAATAACTCGTATTGTACTCGTTGT 57.718 33.333 0.00 0.00 32.47 3.32
1097 1217 0.103755 CAGCTCATCCGCTAGCTTCA 59.896 55.000 13.93 0.00 46.82 3.02
1126 1246 3.508402 TCACCACTAGCGACAGAATTACA 59.492 43.478 0.00 0.00 0.00 2.41
1146 1266 7.157347 GTGTGATAGAATTATCCATCAGCTCA 58.843 38.462 0.00 0.00 34.91 4.26
1147 1267 6.593382 GGTGTGATAGAATTATCCATCAGCTC 59.407 42.308 0.00 0.00 34.91 4.09
1196 1316 0.397816 ATCCTCCTTCTCCACCTCCG 60.398 60.000 0.00 0.00 0.00 4.63
1254 1374 3.149196 CACCACAGTAGGCAAACTCATT 58.851 45.455 0.00 0.00 0.00 2.57
1396 1520 6.962182 TCATCCATCAACTTTAGTTCATCCT 58.038 36.000 0.00 0.00 35.83 3.24
1506 1630 0.884704 GCCACACTCACGGTTGATGT 60.885 55.000 0.00 0.00 0.00 3.06
1760 1886 3.323286 TCACCCCCGAATTGGCGA 61.323 61.111 0.00 0.00 35.87 5.54
1791 1917 0.675633 GCAGCCTCCAAGAAAAAGCA 59.324 50.000 0.00 0.00 0.00 3.91
1801 1927 0.250467 GTGAAGTTCAGCAGCCTCCA 60.250 55.000 5.62 0.00 0.00 3.86
1838 1964 3.696051 CCATCTGGTTGGAAATTCGATGT 59.304 43.478 0.00 0.00 39.25 3.06
2010 2136 6.494952 ACCAACTGATAACCTCTTCTCTAGA 58.505 40.000 0.00 0.00 0.00 2.43
2059 2185 0.322636 ACCAACAACGGACACAACCA 60.323 50.000 0.00 0.00 0.00 3.67
2351 5221 4.749245 AACAAGCATAACGAGAACAAGG 57.251 40.909 0.00 0.00 0.00 3.61
2353 5223 5.493133 ACAAACAAGCATAACGAGAACAA 57.507 34.783 0.00 0.00 0.00 2.83
2360 5230 2.916716 GCATGGACAAACAAGCATAACG 59.083 45.455 0.00 0.00 35.34 3.18
2472 5350 1.833787 TTGAACCCGAGTACCCAGGC 61.834 60.000 0.00 0.00 0.00 4.85
2475 5353 3.307621 GGTTATTTGAACCCGAGTACCCA 60.308 47.826 0.00 0.00 34.26 4.51
2563 5441 4.041444 ACCCTTTGATGAGAGATATGAGCC 59.959 45.833 0.00 0.00 0.00 4.70
2620 5498 9.753674 AATCAGTTTTTCCCAAAGATGTATAGA 57.246 29.630 0.00 0.00 0.00 1.98
2733 5997 2.257409 CTGATGGTTGGTCCCTCCCG 62.257 65.000 0.00 0.00 34.77 5.14
2788 6053 8.564574 ACGTTGAAGACAGAAGCATAAAAATAA 58.435 29.630 0.00 0.00 0.00 1.40
2789 6054 8.094798 ACGTTGAAGACAGAAGCATAAAAATA 57.905 30.769 0.00 0.00 0.00 1.40
2790 6055 6.970484 ACGTTGAAGACAGAAGCATAAAAAT 58.030 32.000 0.00 0.00 0.00 1.82
3004 6271 0.449786 TCATTGTGTAAATGCGCCCG 59.550 50.000 4.18 0.00 0.00 6.13
3006 6273 1.919918 GCTTCATTGTGTAAATGCGCC 59.080 47.619 4.18 0.00 0.00 6.53
3008 6275 2.529151 GGGCTTCATTGTGTAAATGCG 58.471 47.619 0.00 0.00 0.00 4.73
3301 6568 2.049627 ATGGCCGGAGATGAAGAGGC 62.050 60.000 5.05 0.00 46.51 4.70
3474 6741 2.502142 TTCTGCCAGCTGAATCATGT 57.498 45.000 17.39 0.00 0.00 3.21
3486 6753 6.349243 ACTCATTTTCATCATTTTCTGCCA 57.651 33.333 0.00 0.00 0.00 4.92
3755 7037 4.184649 ACTTGAACCACAAAAGAGGGAT 57.815 40.909 0.00 0.00 38.08 3.85
3872 7175 5.933846 TTAGTAGGGAGCTCTATCTTCCT 57.066 43.478 14.64 12.60 44.29 3.36
3925 7914 6.127814 CCATCAGTGTGCAATTTTCTATGTCT 60.128 38.462 0.00 0.00 0.00 3.41
4033 8022 6.906659 AGTCCGCAATGATTTCATATTCATC 58.093 36.000 0.00 0.00 35.10 2.92
4034 8023 6.713903 AGAGTCCGCAATGATTTCATATTCAT 59.286 34.615 0.00 0.00 35.10 2.57
4035 8024 6.017687 CAGAGTCCGCAATGATTTCATATTCA 60.018 38.462 0.00 0.00 35.10 2.57
4049 8038 2.125552 CCATCGCAGAGTCCGCAA 60.126 61.111 0.00 0.00 43.63 4.85
4064 8053 1.339438 GCTCTTCTCCATGTCAAGCCA 60.339 52.381 0.00 0.00 0.00 4.75
4236 8243 0.299895 CTCACGCTCAACATGATCGC 59.700 55.000 0.00 0.00 39.34 4.58
4238 8245 1.929836 GTCCTCACGCTCAACATGATC 59.070 52.381 0.00 0.00 0.00 2.92
4353 8360 1.865788 GCGCAGGCAATTGAGACCAA 61.866 55.000 10.34 0.00 39.62 3.67
4361 8368 1.474077 CTTAAGGAAGCGCAGGCAATT 59.526 47.619 11.47 0.00 43.41 2.32
4464 8471 3.330701 AGCTCTGTAACCAGGGATTTCAA 59.669 43.478 0.00 0.00 42.19 2.69
4478 8485 2.167693 CCGTCCCAAACATAGCTCTGTA 59.832 50.000 5.03 0.00 0.00 2.74
4480 8487 1.656652 CCGTCCCAAACATAGCTCTG 58.343 55.000 0.00 0.00 0.00 3.35
4492 8499 0.471211 CTAGGAATAGCCCCGTCCCA 60.471 60.000 0.00 0.00 37.37 4.37
4495 8502 2.036089 CAGAACTAGGAATAGCCCCGTC 59.964 54.545 0.00 0.00 37.37 4.79
4682 8692 6.321690 ACTGAATCCTTACTAATGTAGAGCGT 59.678 38.462 0.00 0.00 0.00 5.07
4685 8695 8.138712 GTCCACTGAATCCTTACTAATGTAGAG 58.861 40.741 0.00 0.00 0.00 2.43
4689 8699 6.352222 CCTGTCCACTGAATCCTTACTAATGT 60.352 42.308 0.00 0.00 0.00 2.71
4705 8715 0.109342 CCTCTTGCAACCTGTCCACT 59.891 55.000 0.00 0.00 0.00 4.00
4718 8728 2.859273 AATGCGTCCTCGGCCTCTTG 62.859 60.000 0.00 0.00 37.56 3.02
4768 8778 7.386848 TGCTATTAACTAAATATGACGGAAGGC 59.613 37.037 0.00 0.00 42.12 4.35
4782 8795 9.494271 CAGGAATTATGCTCTGCTATTAACTAA 57.506 33.333 0.00 0.00 0.00 2.24
4845 8865 1.955683 GCTGCCCCTTTTACTTCTCCC 60.956 57.143 0.00 0.00 0.00 4.30
4881 8902 1.135083 AGCGGACACAGGTAAAGATCG 60.135 52.381 0.00 0.00 0.00 3.69
4890 8911 0.742281 CTTGATCCAGCGGACACAGG 60.742 60.000 0.00 1.74 32.98 4.00
4891 8912 0.742281 CCTTGATCCAGCGGACACAG 60.742 60.000 0.00 0.00 32.98 3.66
4893 8914 0.036388 TTCCTTGATCCAGCGGACAC 60.036 55.000 0.00 0.00 32.98 3.67
4899 8920 3.857549 GGAAAAGTTCCTTGATCCAGC 57.142 47.619 0.00 0.00 46.57 4.85
4921 9091 3.640967 ACAATTGGCAGTACAACCACATT 59.359 39.130 10.83 7.31 35.10 2.71
4940 9117 6.773976 AAAACAAAGATTCAGAGGACACAA 57.226 33.333 0.00 0.00 0.00 3.33
4948 9125 6.455360 AGCTGTCAAAAACAAAGATTCAGA 57.545 33.333 0.00 0.00 37.45 3.27
4996 9177 6.772716 AGAGAGGCAGATTACAAGAAAAACAA 59.227 34.615 0.00 0.00 0.00 2.83
4998 9179 6.205658 ACAGAGAGGCAGATTACAAGAAAAAC 59.794 38.462 0.00 0.00 0.00 2.43
5026 9207 1.315690 AATCATCAGGATTGCAGCCG 58.684 50.000 2.44 0.00 44.51 5.52
5094 9286 5.368989 AGTATAACTAGACCAAATGCAGCC 58.631 41.667 0.00 0.00 0.00 4.85
5132 9401 2.100216 GCAATTAGCACCGCACCG 59.900 61.111 0.00 0.00 44.79 4.94
5162 9431 0.245539 ACAGGCGCGTACAGTGTTAT 59.754 50.000 8.43 0.00 0.00 1.89
5170 9440 1.850441 CTTATGTACACAGGCGCGTAC 59.150 52.381 8.43 14.15 38.76 3.67
5174 9444 1.006832 CCACTTATGTACACAGGCGC 58.993 55.000 0.00 0.00 0.00 6.53
5175 9445 1.206132 TCCCACTTATGTACACAGGCG 59.794 52.381 0.00 0.00 0.00 5.52
5283 9806 4.332186 ACACGATACGTACAGTGTACAG 57.668 45.455 28.26 22.58 44.79 2.74
5318 9841 6.922957 TGTTAAGTAAGCAAAAATGAAGCCTG 59.077 34.615 0.00 0.00 0.00 4.85
5325 9848 8.931775 GGGGTTTATGTTAAGTAAGCAAAAATG 58.068 33.333 0.00 0.00 0.00 2.32
5329 9852 7.256012 CCAAGGGGTTTATGTTAAGTAAGCAAA 60.256 37.037 0.00 0.00 0.00 3.68
5380 10742 5.433526 ACACAGGCTTAAAAGTGTTGACTA 58.566 37.500 2.04 0.00 42.06 2.59
5381 10743 4.270008 ACACAGGCTTAAAAGTGTTGACT 58.730 39.130 2.04 0.00 42.06 3.41
5382 10744 4.632538 ACACAGGCTTAAAAGTGTTGAC 57.367 40.909 2.04 0.00 42.06 3.18
5383 10745 5.186942 TGTACACAGGCTTAAAAGTGTTGA 58.813 37.500 12.07 0.00 42.06 3.18
5384 10746 5.493133 TGTACACAGGCTTAAAAGTGTTG 57.507 39.130 12.07 0.00 42.06 3.33
5388 10751 6.430000 CCACTTATGTACACAGGCTTAAAAGT 59.570 38.462 0.00 0.00 0.00 2.66
5412 10775 3.963129 TGTACAGTTCCCATCAAATCCC 58.037 45.455 0.00 0.00 0.00 3.85
5479 10842 7.041780 TCACTTGACAAGATTCTGTCTAAAAGC 60.042 37.037 21.95 0.00 45.03 3.51
5520 10883 6.292703 CGTCCCACAATATAAGATCGTTTTCC 60.293 42.308 0.00 0.00 0.00 3.13
5521 10884 6.292703 CCGTCCCACAATATAAGATCGTTTTC 60.293 42.308 0.00 0.00 0.00 2.29
5588 10951 1.134226 CTTTTGCCAGCGCTTCAAAG 58.866 50.000 24.62 18.16 35.36 2.77
5630 10993 6.582636 CAGTTACTGCCATCTTCCTATTGTA 58.417 40.000 0.00 0.00 0.00 2.41
5632 10995 5.998454 CAGTTACTGCCATCTTCCTATTG 57.002 43.478 0.00 0.00 0.00 1.90
5685 11048 6.038271 ACAAATGACAGTTAAGGTTCACAGAC 59.962 38.462 0.00 0.00 0.00 3.51
5686 11049 6.119536 ACAAATGACAGTTAAGGTTCACAGA 58.880 36.000 0.00 0.00 0.00 3.41
5687 11050 6.377327 ACAAATGACAGTTAAGGTTCACAG 57.623 37.500 0.00 0.00 0.00 3.66
5688 11051 6.405286 CCAACAAATGACAGTTAAGGTTCACA 60.405 38.462 0.00 0.00 0.00 3.58
5689 11052 5.977129 CCAACAAATGACAGTTAAGGTTCAC 59.023 40.000 0.00 0.00 0.00 3.18
5690 11053 5.888724 TCCAACAAATGACAGTTAAGGTTCA 59.111 36.000 0.00 0.00 0.00 3.18
5691 11054 6.385649 TCCAACAAATGACAGTTAAGGTTC 57.614 37.500 0.00 0.00 0.00 3.62
5692 11055 6.153680 TGTTCCAACAAATGACAGTTAAGGTT 59.846 34.615 0.00 0.00 35.67 3.50
5693 11056 5.654650 TGTTCCAACAAATGACAGTTAAGGT 59.345 36.000 0.00 0.00 35.67 3.50
5694 11057 6.142818 TGTTCCAACAAATGACAGTTAAGG 57.857 37.500 0.00 0.00 35.67 2.69
5711 11074 1.993956 CCATGGACTTGGTTGTTCCA 58.006 50.000 5.56 0.00 45.60 3.53
5712 11075 0.603065 GCCATGGACTTGGTTGTTCC 59.397 55.000 18.40 0.00 39.11 3.62
5713 11076 1.327303 TGCCATGGACTTGGTTGTTC 58.673 50.000 18.40 0.00 39.11 3.18
5714 11077 1.786937 TTGCCATGGACTTGGTTGTT 58.213 45.000 18.40 0.00 39.11 2.83
5715 11078 1.688197 CTTTGCCATGGACTTGGTTGT 59.312 47.619 18.40 0.00 39.11 3.32
5716 11079 1.001181 CCTTTGCCATGGACTTGGTTG 59.999 52.381 18.40 0.00 39.11 3.77
5717 11080 1.341080 CCTTTGCCATGGACTTGGTT 58.659 50.000 18.40 0.00 39.11 3.67
5718 11081 1.187567 GCCTTTGCCATGGACTTGGT 61.188 55.000 18.40 0.00 39.11 3.67
5719 11082 0.901580 AGCCTTTGCCATGGACTTGG 60.902 55.000 18.40 12.63 38.69 3.61
5720 11083 1.838112 TAGCCTTTGCCATGGACTTG 58.162 50.000 18.40 1.88 38.69 3.16
5721 11084 2.243221 AGATAGCCTTTGCCATGGACTT 59.757 45.455 18.40 0.00 38.69 3.01
5722 11085 1.849039 AGATAGCCTTTGCCATGGACT 59.151 47.619 18.40 4.55 38.69 3.85
5723 11086 2.225467 GAGATAGCCTTTGCCATGGAC 58.775 52.381 18.40 7.64 38.69 4.02
5724 11087 1.143684 GGAGATAGCCTTTGCCATGGA 59.856 52.381 18.40 0.00 38.69 3.41
5725 11088 1.144503 AGGAGATAGCCTTTGCCATGG 59.855 52.381 7.63 7.63 38.69 3.66
5726 11089 2.653234 AGGAGATAGCCTTTGCCATG 57.347 50.000 0.00 0.00 38.69 3.66
5727 11090 4.298103 CATAGGAGATAGCCTTTGCCAT 57.702 45.455 0.00 0.00 39.50 4.40
5728 11091 3.777106 CATAGGAGATAGCCTTTGCCA 57.223 47.619 0.00 0.00 39.50 4.92
5743 11106 1.377994 GCCATCTCCCCTGCATAGG 59.622 63.158 0.00 0.00 44.18 2.57
5744 11107 0.250640 GTGCCATCTCCCCTGCATAG 60.251 60.000 0.00 0.00 35.96 2.23
5745 11108 1.708993 GGTGCCATCTCCCCTGCATA 61.709 60.000 0.00 0.00 35.96 3.14
5746 11109 2.599597 GTGCCATCTCCCCTGCAT 59.400 61.111 0.00 0.00 35.96 3.96
5747 11110 3.731728 GGTGCCATCTCCCCTGCA 61.732 66.667 0.00 0.00 0.00 4.41
5748 11111 3.412624 GAGGTGCCATCTCCCCTGC 62.413 68.421 0.00 0.00 0.00 4.85
5749 11112 2.750657 GGAGGTGCCATCTCCCCTG 61.751 68.421 13.39 0.00 43.71 4.45
5750 11113 2.367512 GGAGGTGCCATCTCCCCT 60.368 66.667 13.39 0.00 43.71 4.79
5754 11117 0.678950 GCTCTAGGAGGTGCCATCTC 59.321 60.000 0.00 0.00 40.02 2.75
5755 11118 0.031716 TGCTCTAGGAGGTGCCATCT 60.032 55.000 0.00 0.00 40.02 2.90
5756 11119 0.392336 CTGCTCTAGGAGGTGCCATC 59.608 60.000 0.00 0.00 40.02 3.51
5757 11120 0.031716 TCTGCTCTAGGAGGTGCCAT 60.032 55.000 0.00 0.00 40.02 4.40
5758 11121 0.685785 CTCTGCTCTAGGAGGTGCCA 60.686 60.000 0.00 0.00 40.02 4.92
5759 11122 2.026945 GCTCTGCTCTAGGAGGTGCC 62.027 65.000 0.00 0.00 34.00 5.01
5760 11123 1.326213 TGCTCTGCTCTAGGAGGTGC 61.326 60.000 0.00 4.91 35.44 5.01
5761 11124 0.746063 CTGCTCTGCTCTAGGAGGTG 59.254 60.000 0.00 0.00 34.00 4.00
5762 11125 0.396974 CCTGCTCTGCTCTAGGAGGT 60.397 60.000 11.23 0.00 44.98 3.85
5763 11126 2.428834 CCTGCTCTGCTCTAGGAGG 58.571 63.158 6.68 6.68 44.77 4.30
5764 11127 0.746063 CACCTGCTCTGCTCTAGGAG 59.254 60.000 0.00 0.00 34.42 3.69
5765 11128 0.685785 CCACCTGCTCTGCTCTAGGA 60.686 60.000 0.00 0.00 34.42 2.94
5766 11129 1.821936 CCACCTGCTCTGCTCTAGG 59.178 63.158 0.00 0.00 36.39 3.02
5767 11130 1.143620 GCCACCTGCTCTGCTCTAG 59.856 63.158 0.00 0.00 36.87 2.43
5768 11131 1.610379 TGCCACCTGCTCTGCTCTA 60.610 57.895 0.00 0.00 42.00 2.43
5769 11132 2.926779 TGCCACCTGCTCTGCTCT 60.927 61.111 0.00 0.00 42.00 4.09
5770 11133 2.745492 GTGCCACCTGCTCTGCTC 60.745 66.667 0.00 0.00 42.00 4.26
5771 11134 4.694233 CGTGCCACCTGCTCTGCT 62.694 66.667 0.00 0.00 42.00 4.24


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.